A question of ERVs

[mark kennedy]

Still can't explain why we don't see ERVs shared orthologously between orangutans and humans, but missing from gorilla and chimp, eh mark? Or why the ERVs which do deviate from the nested hierarchy are non-orthologous, as expected by common ancestry?

Your using a couple of terms fast and loose, there is nothing to explain. The ERVs are a protein coding gene graveyard, very few in the human genome that actually work. This is supposed to be some kind of proof but the evidence is so convoluted there is no coherent argument. Still can't explain how:

With more than 100 members, CERV 1/PTERV1 is one of the most abundant families of endogenous retroviruses in the chimpanzee genome. (Genome Biol. 2006).
​

Or that:

PtERV1-like elements are present in the rhesus monkey, olive baboon and African great apes but not in human, orang-utan or gibbon, suggesting separate germline invasions in these species.

(Initial Sequence of the Chimpanzee Genome, Nature 2005)

Why are the ERVs which are shared by all 4 species among the most mutated? Why are the ones shared only by chimps and humans among the least mutated? Why does this also hold true with LTR divergence?

The evidence is anecdotal at best but if you don't bother with the actual research you don't have to worry about that do you?

Instead of demonstrating how this is remotely possible given the known mutation rate evolutionists would rather talk about this: Phylogenies of seven HERV loci. When 8% of the human genome is made up of ERVs with a 94% nucleotide sequence identity should we really be supprised the seven loci are the same? For HERV-K JML 6.17 they identified 5 substitutions, a couple of them had as many as 10. This is supposed to be some kind of proof?

Here they discuss the probability of the 11 substitutions, assuming they happened by chance:

Although it is possible that any one position may suffer an identical substitution in both LTRs by chance, the probability of 11 positions undergoing identical substitutions in both LTRs is exceedingly low.

Your incredulity is the real diversion here. Because you fail to offer an alternative explanation for the pattern. You simply can't believe, for some reason, that ERVs can be inserted in the germline...despite the fact that USCognito has presented a paper where we are witnessing it happening in REAL TIME with Koalas. And have also been shown examples of ERVs where the mutations were reversed, and resulted in viable viruses.

That's it, the Koalas, that's the extent of ERVs invading germlines and with devastating deleterious effects at that. HIV is a dangerous ERV that invades white blood cells, by all accounts it's deadly dangerous and caused an epidemic in certain circles. Yet we are supposed to believe that 8% of the human genome is the result of them invading sex cells in the germline in the most vulnerable part of the development process because, we want that naturalistic assumption so bad, it doesn't matter what the odds are.

I'm not incredulous, I'm appalled that this would pass for a scientific argument. I've come to admire the science involved and I'm greatly enthusiastic at the level of discovery emerging from the field of genetics. For someone to pass this convoluted hodgepodge of rationalizations and hair brain semantics to pass it off as somehow scientific is ludicrous. It's an affront to anything remotely scientific, I don't understand why you guys aren't embarrassed to make such a baseless homology argument, which is far and away, the worst I've ever seen and I've seen plenty. Charles Darwin must be rolling over in his grave.

 

[pitabread]

Notice the nature of the argument, @xianghua. The nested hierarchy doesn't allow for design, so the pattern requires a naturalistic explanation.

I think some context is needed here.

One of the claims that @xianghua has repeatedly made is that phylogenetic trees from non-living objects that mimic the types of trees that are created based on living organisms.

Using vehicles for his examples, he has suggested that trees would show neat sorting patterns of cars, vans, trucks, etc. And he supports this by posting crudely drawn trees that look like they were created in Paint. What he hasn't done, however, is actually try to create real phylogenetic trees based on physical characteristics of the aforementioned objects.

I was curious to see if his claims would hold up, so I opted to create trees on his behalf. I create a character matrix based on various vehicles and generated trees using the phylogenetic software, Misquite.

See this post: Post #1610 - self-replicating watch thread

My results were two-fold:

1) Vehicles did not sort themselves the way he claimed they would. Vehicles did not sort into neat categories of cars, trucks, vans and so on; at least nothing to show any sort of progression.

2) When creating trees based on subsets of characteristics, I would get wildly different results with zero statistical correlation between trees (see this post).

In a nutshell, his claims about phyogenetic trees and designed objects were shown to be wrong. And it makes sense. Phylogenetic trees are based on inferring hereditary relationships between things. Designed objects like cars and trucks have no hereditary relationship.

If you want to pick up his argument and try to defend, by all means. Nobody else has taken a stab at it.

 

[46AND2]

Your using a couple of terms fast and loose, there is nothing to explain. The ERVs are a protein coding gene graveyard, very few in the human genome that actually work. This is supposed to be some kind of proof but the evidence is so convoluted there is no coherent argument. Still can't explain how:

With more than 100 members, CERV 1/PTERV1 is one of the most abundant families of endogenous retroviruses in the chimpanzee genome. (Genome Biol. 2006).
​

Or that:

PtERV1-like elements are present in the rhesus monkey, olive baboon and African great apes but not in human, orang-utan or gibbon, suggesting separate germline invasions in these species.

(Initial Sequence of the Chimpanzee Genome, Nature 2005)



The evidence is anecdotal at best but if you don't bother with the actual research you don't have to worry about that do you?

Instead of demonstrating how this is remotely possible given the known mutation rate evolutionists would rather talk about this: Phylogenies of seven HERV loci. When 8% of the human genome is made up of ERVs with a 94% nucleotide sequence identity should we really be supprised the seven loci are the same? For HERV-K JML 6.17 they identified 5 substitutions, a couple of them had as many as 10. This is supposed to be some kind of proof?

Here they discuss the probability of the 11 substitutions, assuming they happened by chance:

Although it is possible that any one position may suffer an identical substitution in both LTRs by chance, the probability of 11 positions undergoing identical substitutions in both LTRs is exceedingly low.



That's it, the Koalas, that's the extent of ERVs invading germlines and with devastating deleterious effects at that. HIV is a dangerous ERV that invades white blood cells, by all accounts it's deadly dangerous and caused an epidemic in certain circles. Yet we are supposed to believe that 8% of the human genome is the result of them invading sex cells in the germline in the most vulnerable part of the development process because, we want that naturalistic assumption so bad, it doesn't matter what the odds are.

I'm not incredulous, I'm appalled that this would pass for a scientific argument. I've come to admire the science involved and I'm greatly enthusiastic at the level of discovery emerging from the field of genetics. For someone to pass this convoluted hodgepodge of rationalizations and hair brain semantics to pass it off as somehow scientific is ludicrous. It's an affront to anything remotely scientific, I don't understand why you guys aren't embarrassed to make such a baseless homology argument, which is far and away, the worst I've ever seen and I've seen plenty. Charles Darwin must be rolling over in his grave.

Instead of wasting all that time on that post, you could have just answered that, no, you have no explanation for the questions I asked. But then, that wouldn't have served as a very good diversion tactic like this, would it?

 

[mark kennedy]

Instead of wasting all that time on that post, you could have just answered that, no, you have no explanation for the questions I asked. But then, that wouldn't have served as a very good diversion tactic like this, would it?

You don't have a clue how this is used to trace lineage do you? These markers have nothing to do with common ancestry and you don't even begin to realize that. No one has answers to your questions because they are not real questions, just some terms you don't understand based on a broken bunch of protein coding genes you expect everyone else to accept as germline invasions. It's sad really, you guys could learn so much exploring the real evidence but you go rummaging around a junk yard because you think no one will ever catch you. You have no explanation for major evolutionary adaptation so you waste everyone's time with ERV speculation and throwing around terms you do not understand. Too bad, you could have learned something.

 

[46AND2]

You don't have a clue how this is used to trace lineage do you? These markers have nothing to do with common ancestry and you don't even begin to realize that. No one has answers to your questions because they are not real questions, just some terms you don't understand based on a broken bunch of protein coding genes you expect everyone else to accept as germline invasions. It's sad really, you guys could learn so much exploring the real evidence but you go rummaging around a junk yard because you think no one will ever catch you. You have no explanation for major evolutionary adaptation so you waste everyone's time with ERV speculation and throwing around terms you do not understand. Too bad, you could have learned something.

I don't understand the terms? For a decade geneticists like sfs have explained to you how you are misinterpreting what you are reading. You come up with conclusions on papers that are opposite of what the authors conclude. Yet I'm the one who doesn't understand? While I don't claim to be a professional, by any means, coming from you, that's pretty funny.

Also, I find it amusing that you mention HIV in your last post as an argument for debilitating retroviruses despite the fact that it isn't germline. Yet, when I pointed out that the other major retrovirus that can cause leukemia only does so in 2-4% of those who contract it, and often several decades after infection, you poo-poo'd that because it wasn't germline.

It's very simple. What is the cause of the pattern we see, if not common ancestry? I'm simply asking you to explain an observation.

 

[mark kennedy]

I don't understand the terms? For a decade geneticists like sfs have explained to you how you are misinterpreting what you are reading. You come up with conclusions on papers that are opposite of what the authors conclude. Yet I'm the one who doesn't understand? While I don't claim to be a professional, by any means, coming from you, that's pretty funny.

Also, I find it amusing that you mention HIV in your last post as an argument for debilitating retroviruses despite the fact that it isn't germline. Yet, when I pointed out that the other major retrovirus that can cause leukemia only does so in 2-4% of those who contract it, and often several decades after infection, you poo-poo'd that because it wasn't germline.

It's very simple. What is the cause of the pattern we see, if not common ancestry? I'm simply asking you to explain an observation.

No, your touting a party line and Steve, sfs, has never addressed more then marginal points. The ERVs are marginal points of reference at best and make no attempt to address what caused the adaptive evolution that led from our supposed ape ancestors and this misleading nonsense is hardly an argument. You didn't address anything I raised, typical.

 

[pitabread]

The ERVs are marginal points of reference at best and make no attempt to address what caused the adaptive evolution that led from our supposed ape ancestors

...

It's not supposed to?

It's like complaining that plate tectonics don't explain solar flares. What is the point?

On top of that it's ultimately just falling back on your argument from personal incredulity. There's nothing compelling in the end.

 

[46AND2]

No, your touting a party line and Steve, sfs, has never addressed more then marginal points. The ERVs are marginal points of reference at best and make no attempt to address what caused the adaptive evolution that led from our supposed ape ancestors and this misleading nonsense is hardly an argument. You didn't address anything I raised, typical.

1. The points you raised were a deflection to avoid answering my questions.

2. I've already answered your points earlier in the thread.

3. I pointed out that you are using the same argument for HIV, that you claimed I couldn't use for the mostly benign leukemia retrovirus, since they aren't germline infections.

The only person evading things here is you.

 

[xianghua]

Again, not a nested hierarchy.

actually it is:

where do you see non hierarchy here?

 

[pitabread]

actually it is:

where do you see non hierarchy here?

Real phylogenetic trees that result in nested hierarchies are generated based on data sets.

What you posted in just a picture you drew. Just because you can draw a picture, doesn't mean it is relevant.

When I tried to create phylogenetic trees based on data sets of vehicles, they didn't follow the pattern in the above tree.

How do you explain this?

 

[xianghua]

Notice the nature of the argument, @xianghua. The nested hierarchy doesn't allow for design, so the pattern requires a naturalistic explanation.


At least a million base pairs have been added to the Chimpanzee genome since the split, supposedly, from these highly deleterious invasions yet with no ill effects, which is ludicrous.

yep. this is another interesting point. if these ervs are indeed so fatal (in their initial condition) then how so many of them got into the genome in the first place?

 

[xianghua]

Still can't explain why we don't see ERVs shared orthologously between orangutans and humans, but missing from gorilla and chimp, eh mark?

so if i will give you something that is equivalent to that situation (shared transposons that contradict the species phylogeny), you will admit that evolution is false?

 

[mark kennedy]

yep. this is another interesting point. if these ervs are indeed so fatal (in their initial condition) then how so many of them got into the genome in the first place?

That and if they are so prone to mutations is the human genome across such a broad spectrum permanently fixed, mutations and all. What's more, why are their no instances of a human genome being invaded by ERVs in the germline if our ancestors, and the Chimpanzee ancestors were so prone to them? What we know about ERVs like HIV is that they are highly deleterious, that never gets factored into the statistical probability arguments, and should

 

[pitabread]

What's more, why are their no instances of a human genome being invaded by ERVs in the germline if our ancestors, and the Chimpanzee ancestors were so prone to them?

You're talking about insertions that occurred over millions of years versus modern day study of genomics that's been going on for only a few decades. Apples and oranges.

 

[xianghua]

Real phylogenetic trees that result in nested hierarchies are generated based on data sets.

What you posted in just a picture you drew. Just because you can draw a picture, doesn't mean it is relevant.

When I tried to create phylogenetic trees based on data sets of vehicles, they didn't follow the pattern in the above tree.

How do you explain this?

here is the first step: lets start with a bicycle. do you agree that in general a bicycle is more similar to another bicycle then to a car?

 

[pitabread]

here is the first step: lets start with a bicycle. do you agree that in general a bicycle is more similar to another bicycle then to a car?

This isn't about bicycles. This is about your claim that cars, trucks and vans sort themselves into specific groupings.

But when I constructed a tree based on a dataset of characteristics of such vehicles, they didn't sort themselves into those categories.

Again, how do you explain this?

 

[xianghua]

That and if they are so prone to mutations is the human genome across such a broad spectrum permanently fixed, mutations and all.

what do you mean by that?

 

[xianghua]

This isn't about bicycles. This is about your claim that cars, trucks and vans sort themselves into specific groupings.

But when I constructed a tree based on a dataset of characteristics of such vehicles, they didn't sort themselves into those categories.

Again, how do you explain this?

because you checked only for few traits. by this critieria i can give you many examples in biology too that contradict the accpeted phylogeny. this is why i use a bicycle now because it will be more easy to show you that im correct.

 

[46AND2]

That and if they are so prone to mutations is the human genome across such a broad spectrum permanently fixed, mutations and all. What's more, why are their no instances of a human genome being invaded by ERVs in the germline if our ancestors, and the Chimpanzee ancestors were so prone to them? What we know about ERVs like HIV is that they are highly deleterious, that never gets factored into the statistical probability arguments, and should

There have only been 80-ish endogenization events in the last 6 million years in the human lineage. About once every 75,000 years. It's hardly rampant.

 

[pitabread]

because you checked only for few traits.

I used 14 traits. Why would that not be enough?

by this critieria i can give you many examples in biology too that contradict the accpeted phylogeny.

That's irrelevant. We're talking about your claim about cars, trucks and vans.

this is why i use a bicycle now because it will be more easy to show you that im correct.

Again, irrelevant. We're talking about your claim about cars, trucks and vans.

You're still not explaining the results I got and why it contradicts your claims.